Differential proteomics via probabilistic peptide identification scores

Analytical Chemistry

Volumn 77, Issue 2, 2005, Pages 596-606

  Colinge, Jacques ^a   Chiappe, Diego ^a   Lagache, Sophie ^a   Moniatte, Marc ^a   Bougueleret, Lydie ^a  

^a Geneva Proteomics Inc   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN PLASMA; ISOTOPE LABELING; PEPTIDES; SPECTRUM SAMPLING;

ISOTOPES; PLASMAS; PURIFICATION; STABILITY; STANDARDS;

PROTEINS;

ALCOHOL DEHYDROGENASE; BETA AMYLASE; BETA CASEIN; BETA LACTOGLOBULIN; CYTOCHROME C; GLYCOPROTEIN; HUMAN SERUM ALBUMIN; IMMUNOGLOBULIN G; INSULIN; LEPTIN; LYSOZYME; MYOGLOBIN; PEPTIDE; STABLE ISOTOPE; TRANSFERRIN;

ARTICLE; CONTROLLED STUDY; GEL PERMEATION CHROMATOGRAPHY; HUMAN; ION EXCHANGE CHROMATOGRAPHY; ISOTOPE LABELING; MOLECULAR WEIGHT; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; PLASMA; PROBABILITY; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; STATISTICAL ANALYSIS;

ANIMALS; DATABASES; DATABASES AS TOPIC; HUMANS; LEPTIN; MODELS, STATISTICAL; MYOGLOBIN; PEPTIDES; PLASMA; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 12244270638     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac0488513     Document Type: Article

References (24)

1. Allet, N.; Barrillat, N.; Baussant, T.; Boiteau, C.; Botti, P.; Bougueleret, L; Budin, N.; Canet, D.; Carraud, S.; Chiappe, D.; Christmann, N.; Colinge, J.; Cusin, I.; Dafflon, N.; Depresle, B.; Fasso, I.; Frauchiger, P.; Gaertner, H.; Gleizes, A.; Gonzalez-Couto, E.; Jeandenans, C.; Karmime, A.; Kowall, T.; Lagache, S.; Mahe, E.; Masselot, A.; Mattou, H.; Moniatte, M.; Niknejad, A.; Paolini, M.; Perret, F.; Finaud, N.; Ranno, F.; Raimondi, S.; Reffas, S.; Regamey, P. O.; Rey, P. A.; Rodriguez-Tome, P.; Rose, K.; Rossellat, G.; Saudrais, C.; Schmidt, C.; Villain, M.; Zwahlen, C. Proteomics 2004, 4, 2333-51.
2. Link, A. J.; Eng, J.; Schielte, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III. Nat. Biotechnol. 1999, 17, 676-82.
3. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-7.
4. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Proc. Natl. Acad. Sci. U.S.A 2003, 100, 6940-5.
5. Julka, S.; Regnier, F. J. Proteome Res. 2004, 3, 350-63.
6. Bantscheff, M.; Dumpelfeld, B.; Kuster, B. Rapid Commun. Mass Spectrom. 2004, 18, 869-76.
7. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Nat. Biotechnol. 1999, 17, 994-9.
8. Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T. A.; Hill, L. R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C. H. Anal. Chem. 2003, 75, 4818-26.
9. Sweetman, G.; Schirle, M.; Bantscheff, M.; Rick, J.; Küster, B. Proceedings 52nd ASMS Conf. Mass Spectrom. and Allied Topics.
10. Liu, H.; Sadygov, R. G.; Yates, J. R., III. Anal. Chem. 2004, 76, 4193-201.
11. Colinge, J.; Masselot, A.; Giron, M.; Dessingy, T.; Magnin, J. Proteomics 2003, 3, 1454-63.
12. Colinge, J.; Masselot, A.; Cusin, I.; Mahé, E.; Niknejad, A.; Argoud-Puy, G.; Reffas, S.; Bederr, N.; Gleizes, A.; Key, R-A.; Bougueleret, L Proteomics 2004, 4, 1977-84.
13. Colinge, J.; Masselot, A. DDT: TARGETS 2004, 3, S50-5.
14. Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M. Nucleic Acids Res. 2003, 31, 365-70.
15. Ewens, W.; Grant, G. Statistical Methods in Bioinformatics, Springer: New York, 2001.
16. Jain, N.; Thatte, J.; Braciale, T.; Ley, K.; O'Connell, M.; Lee, J. K. Bioinformatics. 2003, 19, 1945-51.
17. Date, C. J. An Introduction to Database Systems, 8th ed.; Pearson Addison-Wesley: Reading, MA 2003.
18. Yu; A.; Chen, J. The POSTGRES Group, The Postgres95 User Manual; University of California, 1995.
19. Venables, W. N.; Ripley, B. D. Modern Applied Statistics with S-PLUS, 4th ed.; Springer; New York, 2002.
20. Dudoit, S.; Fridlyand, J. Bioinformatics 2003, 19, 1090-9.
21. Kaufman, L.; Rousseeuw, P. J. Finding Groups in Data: An Introduction to Cluster Analysis, Wiley-Interscience: New York, 1990.
22. Kohonen, T. Biol. Cybern. 1982, 43, 59-69.
23. Liotta, L. A.; Ferrari, M.; Petricoin, E. Nature 2003, 425, 905.
24. Baggerly, K. A.; Morris, J. S.; Coombes, K. R. Bioinformatics 2004, 20, 777-85.